Analyse protein sets from 2 samples

Question

[Random_user]

Hello there,

I am new to this field and I am trying to do some analysis on the output of TPP pipeline from the phosphopeptide enrichment of 2 disease samples. I am interested in comparing the protein composition of the 2 samples on one level and to compare the number of phosphorylated sites of the different proteins. Do you have any suggestions for this kind of analysis?

Additional ideas are welcome as well.

Thanks in advance for your help.

Answer 1

[Jean-Karim Heriche]

It is usually better to do this kind of analysis towards testing some hypothesis or answering a biological question. This being said, for exploratory purposes, you could do the typical enrichment analysis for pathways, GO terms and whatever you think could be useful e.g. protein domains. For phosphosites, you could start by counting the number of phosphorylated proteins then the total number of sites you've identified followed by checking how many already known sites you've found (using e.g. Phospho.ELM or PhosphoSitePlus as sources of known sites). You could also do the enrichment analysis on the phsophoproteins. Then you could also go for identification/prediction of putative causal kinases (e.g with PHOXTRACK) then try to figure out if some kinases are activated in one condition vs the other.